# last-dotplot

This script makes a dotplot, a.k.a. Oxford Grid, of pair-wise sequence alignments in MAF or LAST tabular format. It requires the Python Imaging Library to be installed. It can be used like this:

    last-dotplot my-alignments my-plot.png

The output can be in any format supported by the Imaging Library:

    last-dotplot alns alns.gif

## Terminology

last-dotplot shows alignments of one set of sequences against another set of sequences. This document calls a "set of sequences" a "genome", though it need not actually be a genome.

## Options

> `-h, --help` | Show a help message, with default option values, and exit.
> `-v, --verbose` | Show progress messages & data about the plot.
> `-x INT, --width=INT` | Maximum width in pixels.
> `-y INT, --height=INT` | Maximum height in pixels.
> `-m M, --maxseqs=M` | Maximum number of horizontal or vertical sequences. If there are >M sequences, the smallest ones (after cutting) will be discarded.
> `-1 PATTERN, --seq1=PATTERN` | Which sequences to show from the 1st (horizontal) genome.
> `-2 PATTERN, --seq2=PATTERN` | Which sequences to show from the 2nd (vertical) genome.
> `-c COLOR, --forwardcolor=COLOR` | Color for forward alignments.
> `-r COLOR, --reversecolor=COLOR` | Color for reverse alignments.
> `--alignments=FILE` | Read secondary alignments. For example: we could use primary alignment data with one human DNA read aligned to the human genome, and secondary alignment data with the whole chimpanzee versus human genomes. last-dotplot will show the parts of the secondary alignments that are near the primary alignments.
> `--sort1=N` | Put the 1st genome's sequences left-to-right in order of: their appearance in the input (0), their names (1), their lengths (2), the top-to-bottom order of (the midpoints of) their alignments (3). You can use two colon-separated values, e.g. "2:1" to specify 2 for primary and 1 for secondary alignments.
> `--sort2=N` | Put the 2nd genome's sequences top-to-bottom in order of: their appearance in the input (0), their names (1), their lengths (2), the left-to-right order of (the midpoints of) their alignments (3).
> `--strands1=N` | Put the 1st genome's sequences: in forwards orientation (0), in the orientation of most of their aligned bases (1). In the latter case, the labels will be colored (in the same way as the alignments) to indicate the sequences' orientations. You can use two colon-separated values for primary and secondary alignments.
> `--strands2=N` | Put the 2nd genome's sequences: in forwards orientation (0), in the orientation of most of their aligned bases (1).
> `--max-gap1=FRAC` | Maximum unaligned gap in the 1st genome. For example, if two parts of one DNA read align to widely-separated parts of one chromosome, it's probably best to cut the intervening region from the dotplot. FRAC is a fraction of the length of the (primary) alignments. You can specify "inf" to keep all unaligned gaps. You can use two comma-separated values, e.g. "0.5,3" to specify 0.5 for end-gaps (unaligned sequence ends) and 3 for mid-gaps (between alignments). You can use two colon-separated values (each of which may be comma-separated) for primary and secondary alignments.
> `--max-gap2=FRAC` | Maximum unaligned gap in the 2nd genome.
> `--pad=FRAC` | Length of pad to leave when cutting unaligned gaps.
> `-j N, --join=N` | Draw horizontal or vertical lines joining adjacent alignments. 0 means don't join, 1 means draw vertical lines joining alignments that are adjacent in the 1st (horizontal) genome, 2 means draw horizontal lines joining alignments that are adjacent in the 2nd (vertical) genome.
> `--border-pixels=INT` | Number of pixels between sequences.
> `--border-color=COLOR` | Color for pixels between sequences.
> `--margin-color=COLOR` | Color for the margins.

### Text options

> `-f FILE, --fontfile=FILE` | TrueType or OpenType font file.
> `-s SIZE, --fontsize=SIZE` | TrueType or OpenType font size.
> `--labels1=N` | Label the displayed regions of the 1st genome with their: sequence name (0), name:length (1), name:start:length (2), name:start-end (3).
> `--labels2=N` | Label the displayed regions of the 2nd genome with their: sequence name (0), name:length (1), name:start:length (2), name:start-end (3).
> `--rot1=ROT` | Text rotation for the 1st genome: h(orizontal) or v(ertical).
> `--rot2=ROT` | Text rotation for the 2nd genome: h(orizontal) or v(ertical).

### Annotation options

These options read annotations of sequence segments, and draw them as colored horizontal or vertical stripes. This looks good only if the annotations are reasonably sparse: e.g. you can't sensibly view 20000 gene annotations in one small dotplot.

> `--bed1=FILE` | Read BED-format annotations for the 1st genome. They are drawn as stripes, with coordinates given by the first three BED fields. The color is specified by the RGB field if present, else pale red if the strand is "+", pale blue if "-", or pale purple.
> `--bed2=FILE` | Read BED-format annotations for the 2nd genome.
> `--rmsk1=FILE` | Read repeat annotations for the 1st genome, in RepeatMasker .out or rmsk.txt format. The color is pale purple for "low complexity", "simple repeats", and "satellites", else pale red for "+" strand and pale blue for "-" strand.
> `--rmsk2=FILE` | Read repeat annotations for the 2nd genome.

### Gene options

> `--genePred1=FILE` | Read gene annotations for the 1st genome in genePred format.
> `--genePred2=FILE` | Read gene annotations for the 2nd genome.
> `--exon-color=COLOR` | Color for exons.
> `--cds-color=COLOR` | Color for protein-coding regions.

### Unsequenced gap options

Note: these "gaps" are not alignment gaps (indels): they are regions of unknown sequence.

> `--gap1=FILE` | Read unsequenced gaps in the 1st genome from an agp or gap file.
> `--gap2=FILE` | Read unsequenced gaps in the 2nd genome from an agp or gap file.
> `--bridged-color=COLOR` | Color for bridged gaps.
> `--unbridged-color=COLOR` | Color for unbridged gaps.

An unsequenced gap will be shown only if it covers at least one whole pixel.

## Choosing sequences

For example, you can exclude sequences with names like "chrUn_random522" like this:

    last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png

Option "-1" selects sequences from the 1st (horizontal) genome, and "-2" selects sequences from the 2nd (vertical) genome. 'chr[!U]*' is a pattern that specifies names starting with "chr", followed by any character except U, followed by anything.

Pattern | Meaning
`*` | zero or more of any character
`?` | any single character
`[abc]` | any character in abc
`[!abc]` | any character not in abc

If a sequence name has a dot (e.g. "hg19.chr7"), the pattern is compared to both the whole name and the part after the dot.

You can specify more than one pattern, e.g. this gets sequences with names starting in "chr" followed by one or two characters:

    last-dotplot -1 'chr?' -1 'chr??' alns alns.png

You can also specify a sequence range; for example this gets the first 1000 bases of chr9:

    last-dotplot -1 chr9:0-1000 alns alns.png

## Text font

You can improve the font quality by increasing its size, e.g. to 20 points:

> last-dotplot -s20 my-alignments my-plot.png

last-dotplot tries to find a nice font on your computer, but may fail and use an ugly font. You can specify a font like this:

    last-dotplot -f /usr/share/fonts/liberation/LiberationSans-Regular.ttf alns alns.png

## Colors

Colors can be specified in various ways described here.